Starting phenix.real_space_refine
on Fri Feb 14 03:55:41 2025 by dcliebschner
===============================================================================

Processing files:
-------------------------------------------------------------------------------

  Found model, /net/cci-nas-00/data/ceres_data/8j3r_35965/02_2025/8j3r_35965.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8j3r_35965/02_2025/8j3r_35965.map

Processing PHIL parameters:
-------------------------------------------------------------------------------

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.95
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8j3r_35965/02_2025/8j3r_35965.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8j3r_35965/02_2025/8j3r_35965.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8j3r_35965/02_2025/8j3r_35965.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8j3r_35965/02_2025/8j3r_35965.cif"
  }
  resolution = 2.95
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.010 sd=   0.076
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 7
    Type Number    sf(0)   Gaussians
     Zn      1      6.06       5
     P     140      5.49       5
     Mg      3      5.21       5
     S      32      5.16       5
     C    5481      2.51       5
     N    1731      2.21       5
     O    2138      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 9526
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 3429
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 422, 3429
          Classifications: {'peptide': 422}
          Link IDs: {'PTRANS': 10, 'TRANS': 411}
    Chain: "D"
      Number of atoms: 466
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 23, 466
          Classifications: {'DNA': 23}
          Link IDs: {'rna3p': 22}
    Chain: "E"
      Number of atoms: 166
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 8, 166
          Classifications: {'DNA': 8}
          Link IDs: {'rna3p': 7}
    Chain: "C"
      Number of atoms: 2345
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 109, 2345
          Classifications: {'RNA': 109}
          Modifications used: {'rna2p_pur': 10, 'rna2p_pyr': 2, 'rna3p_pur': 56, 'rna3p_pyr': 41}
          Link IDs: {'rna2p': 12, 'rna3p': 96}
    Chain: "B"
      Number of atoms: 3116
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 387, 3116
          Classifications: {'peptide': 387}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PTRANS': 9, 'TRANS': 377}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 39
          Unresolved non-hydrogen angles: 45
          Unresolved non-hydrogen dihedrals: 33
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 19
    Chain: "A"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' MG': 1, ' ZN': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "C"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' MG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   3055  SG  CYS A 372      88.301  55.825  32.384  1.00103.10           S
  ATOM   3076  SG  CYS A 375      91.722  54.642  33.836  1.00 97.25           S
  ATOM   3193  SG  CYS A 391      90.472  58.181  34.340  1.00116.70           S
  ATOM   3215  SG  CYS A 394      91.398  56.126  32.490  1.00100.31           S

  Time building chain proxies: 6.15, per 1000 atoms: 0.65
  Number of scatterers: 9526
  At special positions: 0
  Unit cell: (102.3, 117.7, 113.3, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     Zn      1     29.99
     S      32     16.00
     P     140     15.00
     Mg      3     11.99
     O    2138      8.00
     N    1731      7.00
     C    5481      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.33
  Conformation dependent library (CDL) restraints added in 763.6 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A 501 "
        pdb="ZN    ZN A 501 " - pdb=" SG  CYS A 394 "
        pdb="ZN    ZN A 501 " - pdb=" SG  CYS A 391 "
        pdb="ZN    ZN A 501 " - pdb=" SG  CYS A 372 "
        pdb="ZN    ZN A 501 " - pdb=" SG  CYS A 375 "
      Number of angles added : 6


  1594 Ramachandran restraints generated.
    797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1516

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 8 sheets defined
      49.3% alpha, 17.6% beta
      46 base pairs and 86 stacking pairs defined.
    Time for finding SS restraints: 3.98
  Creating SS restraints...
    Processing helix  chain 'A' and resid 16 through 57
    Processing helix  chain 'A' and resid 61 through 66
    Processing helix  chain 'A' and resid 70 through 80
      removed outlier: 3.628A  pdb=" N   TYR A  74 " --> pdb=" O   ASN A  70 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 87 through 105
      removed outlier: 3.638A  pdb=" N   ALA A  98 " --> pdb=" O   THR A  94 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 105 through 111
    Processing helix  chain 'A' and resid 150 through 157
    Processing helix  chain 'A' and resid 171 through 183
      removed outlier: 4.060A  pdb=" N   THR A 175 " --> pdb=" O   GLY A 171 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   ILE A 176 " --> pdb=" O   ALA A 172 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 196 through 199
    Processing helix  chain 'A' and resid 247 through 268
      removed outlier: 3.759A  pdb=" N   GLU A 251 " --> pdb=" O   GLY A 247 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   ASN A 252 " --> pdb=" O   GLY A 248 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 269 through 271
      No H-bonds generated for 'chain 'A' and resid 269 through 271'
    Processing helix  chain 'A' and resid 272 through 276
    Processing helix  chain 'A' and resid 279 through 284
      removed outlier: 3.632A  pdb=" N   ARG A 283 " --> pdb=" O   GLY A 279 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 284 through 316
    Processing helix  chain 'A' and resid 341 through 356
      removed outlier: 3.569A  pdb=" N   ALA A 356 " --> pdb=" O   LYS A 352 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 400 through 409
    Processing helix  chain 'A' and resid 412 through 420
    Processing helix  chain 'B' and resid 16 through 46
    Processing helix  chain 'B' and resid 50 through 56
      removed outlier: 4.153A  pdb=" N   ASP B  54 " --> pdb=" O   SER B  50 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 70 through 81
      removed outlier: 3.547A  pdb=" N   HIS B  77 " --> pdb=" O   GLY B  73 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   THR B  78 " --> pdb=" O   TYR B  74 " (cutoff:3.500A)
      removed outlier: 3.750A  pdb=" N   THR B  81 " --> pdb=" O   HIS B  77 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 87 through 105
    Processing helix  chain 'B' and resid 105 through 112
    Processing helix  chain 'B' and resid 150 through 157
    Processing helix  chain 'B' and resid 171 through 183
    Processing helix  chain 'B' and resid 247 through 265
    Processing helix  chain 'B' and resid 286 through 317
    Processing helix  chain 'B' and resid 341 through 356
      removed outlier: 3.553A  pdb=" N   GLU B 355 " --> pdb=" O   TYR B 351 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   ALA B 356 " --> pdb=" O   LYS B 352 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 400 through 410
      removed outlier: 3.808A  pdb=" N   ILE B 410 " --> pdb=" O   ARG B 406 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 412 through 420
      removed outlier: 3.851A  pdb=" N   ALA B 418 " --> pdb=" O   ASP B 414 " (cutoff:3.500A)
      removed outlier: 3.822A  pdb=" N   SER B 420 " --> pdb=" O   ILE B 416 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 125 through 127
      removed outlier: 3.507A  pdb=" N   GLN A 191 " --> pdb=" O   ASN A 204 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   LYS A 200 " --> pdb=" O   LYS A 195 " (cutoff:3.500A)
      removed outlier: 4.922A  pdb=" N   TRP A 201 " --> pdb=" O   ILE A   9 " (cutoff:3.500A)
      removed outlier: 6.582A  pdb=" N   ILE A 166 " --> pdb=" O   VAL A  10 " (cutoff:3.500A)
      removed outlier: 7.229A  pdb=" N   SER A 164 " --> pdb=" O   PRO A  12 " (cutoff:3.500A)
      removed outlier: 4.682A  pdb=" N   TYR A 142 " --> pdb=" O   ILE A 167 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 125 through 127
      removed outlier: 3.507A  pdb=" N   GLN A 191 " --> pdb=" O   ASN A 204 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   LYS A 200 " --> pdb=" O   LYS A 195 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 242 through 245
      removed outlier: 3.521A  pdb=" N   ALA A 232 " --> pdb=" O   LEU A 245 " (cutoff:3.500A)
      removed outlier: 6.129A  pdb=" N   MET A 222 " --> pdb=" O   GLN A 322 " (cutoff:3.500A)
      removed outlier: 8.397A  pdb=" N   GLU A 324 " --> pdb=" O   MET A 222 " (cutoff:3.500A)
      removed outlier: 8.742A  pdb=" N   ILE A 224 " --> pdb=" O   GLU A 324 " (cutoff:3.500A)
      removed outlier: 6.356A  pdb=" N   ILE A 321 " --> pdb=" O   ILE A 361 " (cutoff:3.500A)
      removed outlier: 7.166A  pdb=" N   ILE A 363 " --> pdb=" O   ILE A 321 " (cutoff:3.500A)
      removed outlier: 6.209A  pdb=" N   MET A 323 " --> pdb=" O   ILE A 363 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 388 through 390
      removed outlier: 3.638A  pdb=" N   ALA A 398 " --> pdb=" O   PHE A 389 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 2 through 5
      removed outlier: 3.514A  pdb=" N   ALA B 189 " --> pdb=" O   SER B 206 " (cutoff:3.500A)
      removed outlier: 5.966A  pdb=" N   ARG B 208 " --> pdb=" O   VAL B 187 " (cutoff:3.500A)
      removed outlier: 5.783A  pdb=" N   VAL B 187 " --> pdb=" O   ARG B 208 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 9 through 12
      removed outlier: 6.756A  pdb=" N   ILE B 166 " --> pdb=" O   VAL B  10 " (cutoff:3.500A)
      removed outlier: 7.558A  pdb=" N   SER B 164 " --> pdb=" O   PRO B  12 " (cutoff:3.500A)
      removed outlier: 4.800A  pdb=" N   TYR B 142 " --> pdb=" O   ILE B 167 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 242 through 245
      removed outlier: 7.169A  pdb=" N   LEU B 218 " --> pdb=" O   CYS B 318 " (cutoff:3.500A)
      removed outlier: 6.806A  pdb=" N   THR B 320 " --> pdb=" O   LEU B 218 " (cutoff:3.500A)
      removed outlier: 6.488A  pdb=" N   LYS B 220 " --> pdb=" O   THR B 320 " (cutoff:3.500A)
      removed outlier: 7.637A  pdb=" N   GLN B 322 " --> pdb=" O   LYS B 220 " (cutoff:3.500A)
      removed outlier: 6.332A  pdb=" N   MET B 222 " --> pdb=" O   GLN B 322 " (cutoff:3.500A)
      removed outlier: 8.324A  pdb=" N   GLU B 324 " --> pdb=" O   MET B 222 " (cutoff:3.500A)
      removed outlier: 8.620A  pdb=" N   ILE B 224 " --> pdb=" O   GLU B 324 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 388 through 390

    356 hydrogen bonds defined for protein.
    1026 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      114 hydrogen bonds
      212 hydrogen bond angles
      0 basepair planarities
      46 basepair parallelities
      86 stacking parallelities
  Total time for adding SS restraints: 3.86

  Time building geometry restraints manager: 2.75 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        1.21 -     1.33: 2190
        1.33 -     1.45: 2776
        1.45 -     1.57: 4700
        1.57 -     1.69: 277
        1.69 -     1.81: 54
  Bond restraints: 9997
  Sorted by residual:
  bond pdb=" CA  ILE A 163 "
       pdb=" CB  ILE A 163 "
    ideal  model  delta    sigma   weight residual
    1.530  1.542 -0.012 1.11e-02 8.12e+03 1.19e+00
  bond pdb=" CA  ILE A 410 "
       pdb=" CB  ILE A 410 "
    ideal  model  delta    sigma   weight residual
    1.537  1.525  0.013 1.29e-02 6.01e+03 9.67e-01
  bond pdb=" CB  PRO B 365 "
       pdb=" CG  PRO B 365 "
    ideal  model  delta    sigma   weight residual
    1.492  1.539 -0.047 5.00e-02 4.00e+02 8.95e-01
  bond pdb=" C1'  DT E  -7 "
       pdb=" N1   DT E  -7 "
    ideal  model  delta    sigma   weight residual
    1.490  1.518 -0.028 3.00e-02 1.11e+03 8.74e-01
  bond pdb=" CB  VAL A  10 "
       pdb=" CG2 VAL A  10 "
    ideal  model  delta    sigma   weight residual
    1.521  1.496  0.025 3.30e-02 9.18e+02 5.59e-01
  ... (remaining 9992 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.53: 13872
        1.53 -     3.06: 248
        3.06 -     4.58: 17
        4.58 -     6.11: 4
        6.11 -     7.64: 2
  Bond angle restraints: 14143
  Sorted by residual:
  angle pdb=" C   ARG A 197 "
        pdb=" N   LYS A 198 "
        pdb=" CA  LYS A 198 "
      ideal   model   delta    sigma   weight residual
     121.54  127.03   -5.49 1.91e+00 2.74e-01 8.27e+00
  angle pdb=" C1'   U C -45 "
        pdb=" N1    U C -45 "
        pdb=" C2    U C -45 "
      ideal   model   delta    sigma   weight residual
     117.70  125.34   -7.64 3.00e+00 1.11e-01 6.48e+00
  angle pdb=" C2'   U C   6 "
        pdb=" C1'   U C   6 "
        pdb=" N1    U C   6 "
      ideal   model   delta    sigma   weight residual
     112.00  115.56   -3.56 1.50e+00 4.44e-01 5.64e+00
  angle pdb=" N   GLN A 338 "
        pdb=" CA  GLN A 338 "
        pdb=" C   GLN A 338 "
      ideal   model   delta    sigma   weight residual
     112.93  110.33    2.60 1.12e+00 7.97e-01 5.37e+00
  angle pdb=" N   ASN A 158 "
        pdb=" CA  ASN A 158 "
        pdb=" CB  ASN A 158 "
      ideal   model   delta    sigma   weight residual
     113.65  110.33    3.32 1.47e+00 4.63e-01 5.11e+00
  ... (remaining 14138 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.90: 5076
       17.90 -    35.80: 534
       35.80 -    53.71: 264
       53.71 -    71.61: 171
       71.61 -    89.51: 33
  Dihedral angle restraints: 6078
    sinusoidal: 3711
      harmonic: 2367
  Sorted by residual:
  dihedral pdb=" CA  LYS A  11 "
           pdb=" C   LYS A  11 "
           pdb=" N   PRO A  12 "
           pdb=" CA  PRO A  12 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.90   17.10     0      5.00e+00 4.00e-02 1.17e+01
  dihedral pdb=" CA  ASN A 131 "
           pdb=" CB  ASN A 131 "
           pdb=" CG  ASN A 131 "
           pdb=" OD1 ASN A 131 "
      ideal   model   delta sinusoidal    sigma   weight residual
     120.00 -168.80  -71.20     2      2.00e+01 2.50e-03 1.08e+01
  dihedral pdb=" CA  ASP B 364 "
           pdb=" CB  ASP B 364 "
           pdb=" CG  ASP B 364 "
           pdb=" OD1 ASP B 364 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -86.06   56.06     1      2.00e+01 2.50e-03 1.06e+01
  ... (remaining 6075 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.035: 1234
       0.035 -    0.069: 277
       0.069 -    0.104: 87
       0.104 -    0.138: 27
       0.138 -    0.173: 3
  Chirality restraints: 1628
  Sorted by residual:
  chirality pdb=" C1'   G C -83 "
            pdb=" O4'   G C -83 "
            pdb=" C2'   G C -83 "
            pdb=" N9    G C -83 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.46    2.28    0.17 2.00e-01 2.50e+01 7.47e-01
  chirality pdb=" CA  ILE A 116 "
            pdb=" N   ILE A 116 "
            pdb=" C   ILE A 116 "
            pdb=" CB  ILE A 116 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.37e-01
  chirality pdb=" C1'   U C -49 "
            pdb=" O4'   U C -49 "
            pdb=" C2'   U C -49 "
            pdb=" N1    U C -49 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.47    2.32    0.14 2.00e-01 2.50e+01 5.13e-01
  ... (remaining 1625 not shown)

  Planarity restraints: 1293
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   U C   6 "   -0.030 2.00e-02 2.50e+03   1.51e-02 5.12e+00
        pdb=" N1    U C   6 "    0.032 2.00e-02 2.50e+03
        pdb=" C2    U C   6 "    0.004 2.00e-02 2.50e+03
        pdb=" O2    U C   6 "    0.002 2.00e-02 2.50e+03
        pdb=" N3    U C   6 "   -0.001 2.00e-02 2.50e+03
        pdb=" C4    U C   6 "   -0.003 2.00e-02 2.50e+03
        pdb=" O4    U C   6 "   -0.009 2.00e-02 2.50e+03
        pdb=" C5    U C   6 "   -0.001 2.00e-02 2.50e+03
        pdb=" C6    U C   6 "    0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G C -44 "   -0.028 2.00e-02 2.50e+03   1.16e-02 4.04e+00
        pdb=" N9    G C -44 "    0.026 2.00e-02 2.50e+03
        pdb=" C8    G C -44 "    0.004 2.00e-02 2.50e+03
        pdb=" N7    G C -44 "   -0.001 2.00e-02 2.50e+03
        pdb=" C5    G C -44 "    0.001 2.00e-02 2.50e+03
        pdb=" C6    G C -44 "   -0.003 2.00e-02 2.50e+03
        pdb=" O6    G C -44 "   -0.008 2.00e-02 2.50e+03
        pdb=" N1    G C -44 "   -0.003 2.00e-02 2.50e+03
        pdb=" C2    G C -44 "    0.002 2.00e-02 2.50e+03
        pdb=" N2    G C -44 "    0.001 2.00e-02 2.50e+03
        pdb=" N3    G C -44 "    0.005 2.00e-02 2.50e+03
        pdb=" C4    G C -44 "    0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A C   7 "   -0.026 2.00e-02 2.50e+03   1.18e-02 3.86e+00
        pdb=" N9    A C   7 "    0.028 2.00e-02 2.50e+03
        pdb=" C8    A C   7 "    0.004 2.00e-02 2.50e+03
        pdb=" N7    A C   7 "   -0.002 2.00e-02 2.50e+03
        pdb=" C5    A C   7 "   -0.001 2.00e-02 2.50e+03
        pdb=" C6    A C   7 "   -0.003 2.00e-02 2.50e+03
        pdb=" N6    A C   7 "   -0.006 2.00e-02 2.50e+03
        pdb=" N1    A C   7 "   -0.001 2.00e-02 2.50e+03
        pdb=" C2    A C   7 "    0.003 2.00e-02 2.50e+03
        pdb=" N3    A C   7 "    0.004 2.00e-02 2.50e+03
        pdb=" C4    A C   7 "   -0.000 2.00e-02 2.50e+03
  ... (remaining 1290 not shown)

  Histogram of nonbonded interaction distances:
        2.06 -     2.63: 117
        2.63 -     3.20: 7902
        3.20 -     3.76: 16080
        3.76 -     4.33: 22344
        4.33 -     4.90: 33220
  Nonbonded interactions: 79663
  Sorted by model distance:
  nonbonded pdb=" OG  SER A 334 "
            pdb="MG    MG A 502 "
     model   vdw
     2.060 2.170
  nonbonded pdb=" NE2 GLN B 322 "
            pdb=" O   ILE B 408 "
     model   vdw
     2.229 3.120
  nonbonded pdb=" O   LEU B 337 "
            pdb=" OH  TYR B 342 "
     model   vdw
     2.246 3.040
  nonbonded pdb=" O2'   U C -45 "
            pdb=" NZ  LYS B 129 "
     model   vdw
     2.260 3.120
  nonbonded pdb=" O2'   A C -66 "
            pdb=" OE2 GLU B 108 "
     model   vdw
     2.266 3.040
  ... (remaining 79658 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 1 through 58 or resid 65 through 81 or (resid 82 through 8 \ 
3 and (name N or name CA or name C or name O or name CB )) or resid 84 through 1 \ 
60 or (resid 161 and (name N or name CA or name C or name O or name CB )) or res \ 
id 162 through 219 or (resid 220 and (name N or name CA or name C or name O or n \ 
ame CB )) or resid 221 through 224 or (resid 225 and (name N or name CA or name  \ 
C or name O or name CB )) or resid 226 through 243 or (resid 244 and (name N or  \ 
name CA or name C or name O or name CB )) or resid 245 through 257 or (resid 258 \ 
 and (name N or name CA or name C or name O or name CB )) or resid 259 through 2 \ 
65 or resid 285 through 326 or resid 331 or (resid 332 and (name N or name CA or \ 
 name C or name O or name CB )) or resid 333 through 365 or (resid 366 and (name \ 
 N or name CA or name C or name O or name CB )) or resid 367 through 378 or (res \ 
id 379 and (name N or name CA or name C or name O or name CB )) or resid 385 thr \ 
ough 414 or (resid 415 and (name N or name CA or name C or name O or name CB ))  \ 
or resid 416 through 421))
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.110
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.330
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     29.360
  Find NCS groups from input model:        0.290
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:12.540
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   42.810
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4967
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   9997  Z= 0.158
  Angle     :  0.500   7.638  14143  Z= 0.288
  Chirality :  0.036   0.173   1628
  Planarity :  0.003   0.034   1293
  Dihedral  : 20.205  89.510   4562
  Min Nonbonded Distance : 2.060

Molprobity Statistics.
  All-atom Clashscore : 5.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.01 %
    Favored  : 97.99 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 11.01 %
    Favored  : 86.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.87 (0.29), residues: 797
  helix:  1.90 (0.26), residues: 361
  sheet:  0.11 (0.39), residues: 162
  loop : -0.90 (0.37), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A  43 
 HIS   0.003   0.001   HIS A 303 
 PHE   0.007   0.001   PHE B 102 
 TYR   0.011   0.001   TYR A 119 
 ARG   0.002   0.000   ARG B 197 

*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1594 Ramachandran restraints generated.
    797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1594 Ramachandran restraints generated.
    797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 152
  time to evaluate  : 0.835 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  204 ASN cc_start: 0.6649 (OUTLIER) cc_final: 0.6447 (m110)
REVERT: A  377 ASN cc_start: 0.6732 (t0) cc_final: 0.6497 (t0)
REVERT: B  141 ASP cc_start: 0.6652 (OUTLIER) cc_final: 0.6234 (m-30)
REVERT: B  142 TYR cc_start: 0.2634 (m-80) cc_final: 0.1486 (m-80)
REVERT: B  288 GLU cc_start: 0.4753 (OUTLIER) cc_final: 0.4004 (tm-30)
  outliers start: 17
  outliers final: 2
  residues processed: 164
  average time/residue: 1.3080
  time to fit residues: 228.4026
Evaluate side-chains
  113 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 108
  time to evaluate  : 0.936 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  204 ASN
Chi-restraints excluded: chain B residue  141 ASP
Chi-restraints excluded: chain B residue  236 PHE
Chi-restraints excluded: chain B residue  288 GLU
Chi-restraints excluded: chain B residue  320 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 77 optimal weight:    0.9990
   chunk 69 optimal weight:    0.0020
   chunk 38 optimal weight:    1.9990
   chunk 23 optimal weight:    6.9990
   chunk 47 optimal weight:    8.9990
   chunk 37 optimal weight:    0.8980
   chunk 72 optimal weight:    7.9990
   chunk 27 optimal weight:   10.0000
   chunk 43 optimal weight:    5.9990
   chunk 53 optimal weight:    7.9990
   chunk 83 optimal weight:    6.9990
   overall best weight:    1.9794

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
B  29 GLN
B  77 HIS
B 194 HIS
B 403 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3988 r_free = 0.3988 target = 0.151674 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.125797 restraints weight = 15561.823|
|-----------------------------------------------------------------------------|
r_work (start): 0.3639 rms_B_bonded: 1.99
r_work: 0.3514 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work (final): 0.3514
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7188
moved from start:          0.7546

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.075   9997  Z= 0.373
  Angle     :  0.823  10.551  14143  Z= 0.442
  Chirality :  0.046   0.174   1628
  Planarity :  0.006   0.054   1293
  Dihedral  : 21.930  85.572   2941
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 9.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  3.77 %
    Allowed  : 16.52 %
    Favored  : 79.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.14 (0.28), residues: 797
  helix:  1.04 (0.25), residues: 378
  sheet: -0.66 (0.39), residues: 140
  loop : -1.30 (0.34), residues: 279

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.003   TRP B  43 
 HIS   0.008   0.003   HIS A 139 
 PHE   0.026   0.004   PHE A 253 
 TYR   0.019   0.003   TYR B 202 
 ARG   0.014   0.001   ARG B 111 

*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1594 Ramachandran restraints generated.
    797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1594 Ramachandran restraints generated.
    797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  233 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 207
  time to evaluate  : 0.816 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   11 LYS cc_start: 0.9049 (ptpt) cc_final: 0.8838 (ptmt)
REVERT: A   14 ASP cc_start: 0.7449 (t0) cc_final: 0.7141 (t70)
REVERT: A   82 LYS cc_start: 0.8107 (mttt) cc_final: 0.7868 (mttt)
REVERT: A  100 ASP cc_start: 0.7791 (m-30) cc_final: 0.7350 (m-30)
REVERT: A  120 LYS cc_start: 0.8003 (pttt) cc_final: 0.7764 (pttt)
REVERT: A  288 GLU cc_start: 0.7128 (tm-30) cc_final: 0.6908 (tm-30)
REVERT: A  294 ILE cc_start: 0.8712 (mt) cc_final: 0.8412 (mp)
REVERT: A  323 MET cc_start: 0.8403 (mtm) cc_final: 0.8199 (mtm)
REVERT: A  332 ILE cc_start: 0.6715 (OUTLIER) cc_final: 0.6454 (pp)
REVERT: A  351 TYR cc_start: 0.7183 (OUTLIER) cc_final: 0.6546 (t80)
REVERT: A  366 GLN cc_start: 0.7397 (tt0) cc_final: 0.7179 (tp-100)
REVERT: B  196 ASP cc_start: 0.5406 (OUTLIER) cc_final: 0.4965 (p0)
REVERT: B  312 MET cc_start: 0.7020 (mmm) cc_final: 0.6204 (mmt)
REVERT: B  323 MET cc_start: 0.3931 (ptm) cc_final: 0.3725 (ptm)
REVERT: B  355 GLU cc_start: 0.6121 (mt-10) cc_final: 0.5746 (mt-10)
  outliers start: 26
  outliers final: 7
  residues processed: 219
  average time/residue: 1.3854
  time to fit residues: 322.0764
Evaluate side-chains
  174 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 164
  time to evaluate  : 0.856 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  149 LEU
Chi-restraints excluded: chain A residue  332 ILE
Chi-restraints excluded: chain A residue  351 TYR
Chi-restraints excluded: chain B residue    4 VAL
Chi-restraints excluded: chain B residue  108 GLU
Chi-restraints excluded: chain B residue  159 VAL
Chi-restraints excluded: chain B residue  196 ASP
Chi-restraints excluded: chain B residue  233 TYR
Chi-restraints excluded: chain B residue  246 GLU
Chi-restraints excluded: chain B residue  320 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 70 optimal weight:    2.9990
   chunk 47 optimal weight:    8.9990
   chunk 54 optimal weight:    0.9990
   chunk 21 optimal weight:    0.5980
   chunk 66 optimal weight:    3.9990
   chunk 43 optimal weight:    4.9990
   chunk 50 optimal weight:    8.9990
   chunk 52 optimal weight:   10.0000
   chunk 4 optimal weight:    0.8980
   chunk 71 optimal weight:    0.9990
   chunk 14 optimal weight:    4.9990
   overall best weight:    1.2986

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A  93 GLN
A 106 GLN
** A 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 347 GLN
B 322 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3897 r_free = 0.3897 target = 0.145392 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.117741 restraints weight = 15351.221|
|-----------------------------------------------------------------------------|
r_work (start): 0.3500 rms_B_bonded: 1.99
r_work: 0.3365 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work (final): 0.3365
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7554
moved from start:          0.9335

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9997  Z= 0.211
  Angle     :  0.590   7.615  14143  Z= 0.317
  Chirality :  0.039   0.164   1628
  Planarity :  0.004   0.049   1293
  Dihedral  : 21.695  88.850   2932
  Min Nonbonded Distance : 2.199

Molprobity Statistics.
  All-atom Clashscore : 8.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.51 %
    Favored  : 98.49 %
  Rotamer:
    Outliers :  3.62 %
    Allowed  : 24.49 %
    Favored  : 71.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.00 (0.28), residues: 797
  helix:  2.25 (0.25), residues: 371
  sheet: -0.00 (0.39), residues: 157
  loop : -1.23 (0.34), residues: 269

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP B  17 
 HIS   0.007   0.001   HIS A 278 
 PHE   0.008   0.001   PHE A 253 
 TYR   0.024   0.002   TYR B 233 
 ARG   0.011   0.001   ARG A 121 

*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1594 Ramachandran restraints generated.
    797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1594 Ramachandran restraints generated.
    797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  217 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 192
  time to evaluate  : 0.939 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 ASP cc_start: 0.7603 (t0) cc_final: 0.7374 (t70)
REVERT: A   28 GLN cc_start: 0.8175 (mt0) cc_final: 0.7885 (mt0)
REVERT: A  121 ARG cc_start: 0.7641 (ptm-80) cc_final: 0.7403 (ptm-80)
REVERT: A  134 VAL cc_start: 0.8218 (p) cc_final: 0.7949 (t)
REVERT: A  150 SER cc_start: 0.8424 (t) cc_final: 0.8196 (p)
REVERT: A  160 LYS cc_start: 0.8405 (ttpp) cc_final: 0.7810 (ttpp)
REVERT: A  161 ARG cc_start: 0.7664 (mmt90) cc_final: 0.7340 (mmm-85)
REVERT: A  197 ARG cc_start: 0.8733 (tmt90) cc_final: 0.8396 (ttp-170)
REVERT: A  220 LYS cc_start: 0.7854 (mttt) cc_final: 0.7606 (mmtp)
REVERT: A  261 ARG cc_start: 0.7780 (OUTLIER) cc_final: 0.7354 (ttp80)
REVERT: A  323 MET cc_start: 0.8607 (OUTLIER) cc_final: 0.8373 (mtm)
REVERT: A  342 TYR cc_start: 0.8065 (m-80) cc_final: 0.7750 (m-80)
REVERT: A  351 TYR cc_start: 0.7072 (OUTLIER) cc_final: 0.6687 (t80)
REVERT: A  355 GLU cc_start: 0.7819 (tp30) cc_final: 0.7443 (tt0)
REVERT: B  103 LYS cc_start: 0.8293 (tppp) cc_final: 0.8031 (ttmm)
REVERT: B  311 ASP cc_start: 0.7842 (m-30) cc_final: 0.7570 (m-30)
REVERT: B  312 MET cc_start: 0.7162 (mmm) cc_final: 0.6447 (mmt)
REVERT: B  323 MET cc_start: 0.5690 (ptm) cc_final: 0.5425 (ptm)
  outliers start: 25
  outliers final: 8
  residues processed: 205
  average time/residue: 1.3973
  time to fit residues: 304.0327
Evaluate side-chains
  179 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 168
  time to evaluate  : 0.834 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  126 ASP
Chi-restraints excluded: chain A residue  182 SER
Chi-restraints excluded: chain A residue  261 ARG
Chi-restraints excluded: chain A residue  323 MET
Chi-restraints excluded: chain A residue  351 TYR
Chi-restraints excluded: chain B residue   39 THR
Chi-restraints excluded: chain B residue  134 VAL
Chi-restraints excluded: chain B residue  233 TYR
Chi-restraints excluded: chain B residue  239 THR
Chi-restraints excluded: chain B residue  246 GLU
Chi-restraints excluded: chain B residue  358 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 2 optimal weight:    0.9990
   chunk 41 optimal weight:    7.9990
   chunk 19 optimal weight:    0.9990
   chunk 65 optimal weight:    2.9990
   chunk 12 optimal weight:    5.9990
   chunk 50 optimal weight:   10.0000
   chunk 63 optimal weight:    5.9990
   chunk 53 optimal weight:    8.9990
   chunk 27 optimal weight:   10.0000
   chunk 48 optimal weight:    9.9990
   chunk 61 optimal weight:    3.9990
   overall best weight:    2.9990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A  87 ASN
A  93 GLN
A 131 ASN
A 155 GLN
A 186 GLN
** A 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 346 GLN
A 347 GLN
B  77 HIS
B 252 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.132238 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.103087 restraints weight = 14822.823|
|-----------------------------------------------------------------------------|
r_work (start): 0.3333 rms_B_bonded: 2.01
r_work: 0.3195 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.3039 rms_B_bonded: 4.89 restraints_weight: 0.2500
r_work (final): 0.3039
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8098
moved from start:          1.2339

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.064   9997  Z= 0.334
  Angle     :  0.688   9.685  14143  Z= 0.363
  Chirality :  0.043   0.167   1628
  Planarity :  0.005   0.048   1293
  Dihedral  : 21.623  84.207   2931
  Min Nonbonded Distance : 1.849

Molprobity Statistics.
  All-atom Clashscore : 9.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  6.81 %
    Allowed  : 24.20 %
    Favored  : 68.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.68 (0.28), residues: 797
  helix:  1.85 (0.25), residues: 377
  sheet: -0.22 (0.39), residues: 153
  loop : -1.15 (0.35), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.003   TRP B  45 
 HIS   0.014   0.002   HIS A 278 
 PHE   0.010   0.002   PHE A 253 
 TYR   0.034   0.002   TYR B 233 
 ARG   0.016   0.001   ARG A 111 

*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1594 Ramachandran restraints generated.
    797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1594 Ramachandran restraints generated.
    797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  257 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 210
  time to evaluate  : 0.834 
Fit side-chains
   revert: symmetry clash
REVERT: A   14 ASP cc_start: 0.8223 (t0) cc_final: 0.7933 (t0)
REVERT: A   50 SER cc_start: 0.8367 (m) cc_final: 0.8071 (t)
REVERT: A  129 LYS cc_start: 0.9353 (OUTLIER) cc_final: 0.9102 (ttmm)
REVERT: A  136 ARG cc_start: 0.8453 (OUTLIER) cc_final: 0.7993 (ttm-80)
REVERT: A  137 MET cc_start: 0.8444 (mmm) cc_final: 0.8066 (mmm)
REVERT: A  161 ARG cc_start: 0.8048 (mmt90) cc_final: 0.7783 (mtp85)
REVERT: A  182 SER cc_start: 0.9026 (OUTLIER) cc_final: 0.8799 (p)
REVERT: A  197 ARG cc_start: 0.8892 (tmt90) cc_final: 0.8650 (ttp-170)
REVERT: A  240 PRO cc_start: 0.9325 (Cg_endo) cc_final: 0.9125 (Cg_exo)
REVERT: A  246 GLU cc_start: 0.8088 (mp0) cc_final: 0.7848 (mp0)
REVERT: A  261 ARG cc_start: 0.8325 (OUTLIER) cc_final: 0.7983 (ttp80)
REVERT: A  262 ILE cc_start: 0.8591 (mt) cc_final: 0.8365 (mm)
REVERT: A  288 GLU cc_start: 0.8020 (tm-30) cc_final: 0.7528 (tm-30)
REVERT: A  347 GLN cc_start: 0.8532 (tp40) cc_final: 0.8327 (tp40)
REVERT: A  406 ARG cc_start: 0.8091 (OUTLIER) cc_final: 0.7873 (ttp80)
REVERT: A  420 SER cc_start: 0.7906 (m) cc_final: 0.7586 (p)
REVERT: B    1 MET cc_start: 0.6674 (OUTLIER) cc_final: 0.6273 (OUTLIER)
REVERT: B   22 THR cc_start: 0.8639 (m) cc_final: 0.8341 (p)
REVERT: B   31 THR cc_start: 0.8626 (OUTLIER) cc_final: 0.8224 (p)
REVERT: B   39 THR cc_start: 0.8935 (OUTLIER) cc_final: 0.8553 (p)
REVERT: B  103 LYS cc_start: 0.8471 (OUTLIER) cc_final: 0.8256 (ttmm)
REVERT: B  118 SER cc_start: 0.8865 (t) cc_final: 0.8597 (p)
REVERT: B  120 LYS cc_start: 0.9001 (mmmm) cc_final: 0.8586 (tppp)
REVERT: B  150 SER cc_start: 0.8333 (t) cc_final: 0.7964 (p)
REVERT: B  155 GLN cc_start: 0.7530 (tp-100) cc_final: 0.7235 (tp-100)
REVERT: B  157 MET cc_start: 0.8614 (mpp) cc_final: 0.7985 (mpp)
REVERT: B  233 TYR cc_start: 0.8142 (OUTLIER) cc_final: 0.7840 (m-80)
REVERT: B  249 GLU cc_start: 0.7069 (tp30) cc_final: 0.6809 (tp30)
REVERT: B  315 LYS cc_start: 0.8387 (OUTLIER) cc_final: 0.8139 (ttpt)
REVERT: B  344 ASP cc_start: 0.7800 (t0) cc_final: 0.7501 (t70)
REVERT: B  401 ASP cc_start: 0.6898 (m-30) cc_final: 0.6663 (m-30)
  outliers start: 47
  outliers final: 7
  residues processed: 234
  average time/residue: 1.5067
  time to fit residues: 372.0005
Evaluate side-chains
  214 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 197
  time to evaluate  : 0.805 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  129 LYS
Chi-restraints excluded: chain A residue  136 ARG
Chi-restraints excluded: chain A residue  182 SER
Chi-restraints excluded: chain A residue  257 VAL
Chi-restraints excluded: chain A residue  261 ARG
Chi-restraints excluded: chain A residue  351 TYR
Chi-restraints excluded: chain A residue  394 CYS
Chi-restraints excluded: chain A residue  406 ARG
Chi-restraints excluded: chain B residue    1 MET
Chi-restraints excluded: chain B residue   31 THR
Chi-restraints excluded: chain B residue   39 THR
Chi-restraints excluded: chain B residue  103 LYS
Chi-restraints excluded: chain B residue  230 VAL
Chi-restraints excluded: chain B residue  233 TYR
Chi-restraints excluded: chain B residue  246 GLU
Chi-restraints excluded: chain B residue  310 VAL
Chi-restraints excluded: chain B residue  315 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 20 optimal weight:    1.9990
   chunk 58 optimal weight:    2.9990
   chunk 65 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9980
   chunk 33 optimal weight:    0.1980
   chunk 69 optimal weight:    4.9990
   chunk 13 optimal weight:    2.9990
   chunk 80 optimal weight:    5.9990
   chunk 46 optimal weight:    8.9990
   chunk 68 optimal weight:    0.9990
   chunk 6 optimal weight:    3.9990
   overall best weight:    1.2386

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A  87 ASN
A  93 GLN
A 131 ASN
A 186 GLN
** A 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 256 GLN
** B 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.137810 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.109106 restraints weight = 14824.908|
|-----------------------------------------------------------------------------|
r_work (start): 0.3371 rms_B_bonded: 1.96
r_work: 0.3233 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work: 0.3078 rms_B_bonded: 4.91 restraints_weight: 0.2500
r_work (final): 0.3078
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8061
moved from start:          1.2580

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   9997  Z= 0.175
  Angle     :  0.564   8.478  14143  Z= 0.304
  Chirality :  0.039   0.155   1628
  Planarity :  0.005   0.070   1293
  Dihedral  : 21.500  86.287   2931
  Min Nonbonded Distance : 2.045

Molprobity Statistics.
  All-atom Clashscore : 7.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Rotamer:
    Outliers :  4.64 %
    Allowed  : 28.55 %
    Favored  : 66.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.28 (0.29), residues: 797
  helix:  2.51 (0.25), residues: 375
  sheet:  0.06 (0.40), residues: 147
  loop : -1.09 (0.35), residues: 275

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B  45 
 HIS   0.007   0.001   HIS A 278 
 PHE   0.009   0.001   PHE A 253 
 TYR   0.011   0.001   TYR B 185 
 ARG   0.014   0.001   ARG B 170 

*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1594 Ramachandran restraints generated.
    797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1594 Ramachandran restraints generated.
    797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  245 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 213
  time to evaluate  : 0.816 
Fit side-chains
REVERT: A   14 ASP cc_start: 0.8285 (t0) cc_final: 0.7997 (t0)
REVERT: A   50 SER cc_start: 0.8266 (OUTLIER) cc_final: 0.8003 (t)
REVERT: A  136 ARG cc_start: 0.8321 (OUTLIER) cc_final: 0.7968 (ttt90)
REVERT: A  137 MET cc_start: 0.8374 (mmm) cc_final: 0.8035 (mmm)
REVERT: A  161 ARG cc_start: 0.8084 (mmt90) cc_final: 0.7812 (mtp85)
REVERT: A  178 ASP cc_start: 0.8642 (m-30) cc_final: 0.8340 (m-30)
REVERT: A  240 PRO cc_start: 0.9372 (Cg_endo) cc_final: 0.9170 (Cg_exo)
REVERT: A  246 GLU cc_start: 0.7912 (mp0) cc_final: 0.7685 (mp0)
REVERT: A  261 ARG cc_start: 0.8374 (OUTLIER) cc_final: 0.8072 (ttp80)
REVERT: A  288 GLU cc_start: 0.7970 (tm-30) cc_final: 0.7582 (tm-30)
REVERT: A  420 SER cc_start: 0.7868 (m) cc_final: 0.7577 (p)
REVERT: B    9 ILE cc_start: 0.8232 (pt) cc_final: 0.7733 (mt)
REVERT: B   22 THR cc_start: 0.8633 (m) cc_final: 0.8424 (p)
REVERT: B  103 LYS cc_start: 0.8409 (tppp) cc_final: 0.8195 (ttmm)
REVERT: B  118 SER cc_start: 0.8675 (t) cc_final: 0.8375 (p)
REVERT: B  120 LYS cc_start: 0.8939 (mmmm) cc_final: 0.8666 (tppp)
REVERT: B  150 SER cc_start: 0.8296 (t) cc_final: 0.7940 (p)
REVERT: B  157 MET cc_start: 0.8619 (mpp) cc_final: 0.8083 (mpp)
REVERT: B  178 ASP cc_start: 0.7660 (m-30) cc_final: 0.7343 (m-30)
REVERT: B  200 LYS cc_start: 0.8010 (mttt) cc_final: 0.7751 (mttt)
REVERT: B  233 TYR cc_start: 0.8120 (OUTLIER) cc_final: 0.7325 (t80)
REVERT: B  249 GLU cc_start: 0.7167 (tp30) cc_final: 0.6773 (tp30)
REVERT: B  346 GLN cc_start: 0.8057 (tt0) cc_final: 0.7683 (tp40)
REVERT: B  401 ASP cc_start: 0.6887 (m-30) cc_final: 0.6450 (m-30)
  outliers start: 32
  outliers final: 11
  residues processed: 226
  average time/residue: 1.4758
  time to fit residues: 352.2374
Evaluate side-chains
  217 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 202
  time to evaluate  : 0.793 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 SER
Chi-restraints excluded: chain A residue   54 ASP
Chi-restraints excluded: chain A residue  136 ARG
Chi-restraints excluded: chain A residue  257 VAL
Chi-restraints excluded: chain A residue  261 ARG
Chi-restraints excluded: chain A residue  394 CYS
Chi-restraints excluded: chain B residue    1 MET
Chi-restraints excluded: chain B residue   31 THR
Chi-restraints excluded: chain B residue   39 THR
Chi-restraints excluded: chain B residue  193 ILE
Chi-restraints excluded: chain B residue  214 ARG
Chi-restraints excluded: chain B residue  233 TYR
Chi-restraints excluded: chain B residue  246 GLU
Chi-restraints excluded: chain B residue  310 VAL
Chi-restraints excluded: chain B residue  324 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 50 optimal weight:   10.0000
   chunk 6 optimal weight:    3.9990
   chunk 9 optimal weight:    4.9990
   chunk 65 optimal weight:    3.9990
   chunk 5 optimal weight:    0.9990
   chunk 70 optimal weight:    4.9990
   chunk 77 optimal weight:    0.9990
   chunk 47 optimal weight:   10.0000
   chunk 56 optimal weight:    5.9990
   chunk 13 optimal weight:    9.9990
   chunk 29 optimal weight:    7.9990
   overall best weight:    2.9990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A  26 GLN
A  87 ASN
A  93 GLN
A 131 ASN
A 204 ASN
** A 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 346 GLN
A 377 ASN
A 403 ASN
B  36 ASN
B  72 HIS
** B  87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 155 GLN
B 256 GLN
B 322 GLN
** B 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 13

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.132547 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.104001 restraints weight = 14785.262|
|-----------------------------------------------------------------------------|
r_work (start): 0.3291 rms_B_bonded: 1.96
r_work: 0.3149 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.2990 rms_B_bonded: 4.88 restraints_weight: 0.2500
r_work (final): 0.2990
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8148
moved from start:          1.3142

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   9997  Z= 0.308
  Angle     :  0.619   6.696  14143  Z= 0.331
  Chirality :  0.041   0.168   1628
  Planarity :  0.005   0.064   1293
  Dihedral  : 21.506  83.272   2931
  Min Nonbonded Distance : 1.978

Molprobity Statistics.
  All-atom Clashscore : 8.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  6.09 %
    Allowed  : 29.13 %
    Favored  : 64.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.15 (0.29), residues: 797
  helix:  2.36 (0.26), residues: 379
  sheet: -0.06 (0.40), residues: 153
  loop : -1.12 (0.34), residues: 265

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B  45 
 HIS   0.008   0.001   HIS A 278 
 PHE   0.009   0.002   PHE A 253 
 TYR   0.015   0.002   TYR B 402 
 ARG   0.012   0.001   ARG A 111 

*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1594 Ramachandran restraints generated.
    797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1594 Ramachandran restraints generated.
    797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  242 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 200
  time to evaluate  : 0.866 
Fit side-chains
REVERT: A   50 SER cc_start: 0.8302 (OUTLIER) cc_final: 0.8080 (t)
REVERT: A  136 ARG cc_start: 0.8356 (OUTLIER) cc_final: 0.8132 (ttm-80)
REVERT: A  137 MET cc_start: 0.8542 (mmm) cc_final: 0.8188 (mmm)
REVERT: A  141 ASP cc_start: 0.8275 (p0) cc_final: 0.8048 (p0)
REVERT: A  161 ARG cc_start: 0.8162 (mmt90) cc_final: 0.7888 (mtp85)
REVERT: A  246 GLU cc_start: 0.7979 (mp0) cc_final: 0.7753 (mp0)
REVERT: A  261 ARG cc_start: 0.8457 (OUTLIER) cc_final: 0.8146 (ttp80)
REVERT: A  270 TYR cc_start: 0.8599 (p90) cc_final: 0.8125 (p90)
REVERT: A  288 GLU cc_start: 0.7956 (tm-30) cc_final: 0.7540 (tm-30)
REVERT: A  351 TYR cc_start: 0.7561 (OUTLIER) cc_final: 0.7252 (t80)
REVERT: A  355 GLU cc_start: 0.8385 (tp30) cc_final: 0.8083 (tp30)
REVERT: A  406 ARG cc_start: 0.7996 (OUTLIER) cc_final: 0.7649 (ttp80)
REVERT: A  420 SER cc_start: 0.7949 (m) cc_final: 0.7639 (p)
REVERT: B    6 ARG cc_start: 0.8184 (mtm-85) cc_final: 0.7856 (ttp-110)
REVERT: B   69 THR cc_start: 0.9040 (OUTLIER) cc_final: 0.8784 (p)
REVERT: B  103 LYS cc_start: 0.8474 (tppp) cc_final: 0.8257 (ttmm)
REVERT: B  118 SER cc_start: 0.8817 (t) cc_final: 0.8489 (p)
REVERT: B  120 LYS cc_start: 0.9029 (mmmm) cc_final: 0.8773 (tppp)
REVERT: B  150 SER cc_start: 0.8302 (t) cc_final: 0.8088 (t)
REVERT: B  157 MET cc_start: 0.8634 (mpp) cc_final: 0.8200 (mpp)
REVERT: B  178 ASP cc_start: 0.7853 (m-30) cc_final: 0.7478 (m-30)
REVERT: B  233 TYR cc_start: 0.8162 (OUTLIER) cc_final: 0.7471 (t80)
REVERT: B  249 GLU cc_start: 0.7164 (tp30) cc_final: 0.6796 (tp30)
REVERT: B  289 GLN cc_start: 0.7523 (tp40) cc_final: 0.7268 (tp40)
REVERT: B  315 LYS cc_start: 0.8492 (tttt) cc_final: 0.8246 (tttt)
REVERT: B  416 ILE cc_start: 0.8117 (pp) cc_final: 0.7821 (mt)
  outliers start: 42
  outliers final: 18
  residues processed: 225
  average time/residue: 1.5922
  time to fit residues: 379.4144
Evaluate side-chains
  218 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 193
  time to evaluate  : 0.806 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 SER
Chi-restraints excluded: chain A residue   70 ASN
Chi-restraints excluded: chain A residue   79 ILE
Chi-restraints excluded: chain A residue  114 MET
Chi-restraints excluded: chain A residue  136 ARG
Chi-restraints excluded: chain A residue  150 SER
Chi-restraints excluded: chain A residue  257 VAL
Chi-restraints excluded: chain A residue  261 ARG
Chi-restraints excluded: chain A residue  318 CYS
Chi-restraints excluded: chain A residue  351 TYR
Chi-restraints excluded: chain A residue  394 CYS
Chi-restraints excluded: chain A residue  406 ARG
Chi-restraints excluded: chain B residue   31 THR
Chi-restraints excluded: chain B residue   39 THR
Chi-restraints excluded: chain B residue   69 THR
Chi-restraints excluded: chain B residue   81 THR
Chi-restraints excluded: chain B residue  114 MET
Chi-restraints excluded: chain B residue  132 ILE
Chi-restraints excluded: chain B residue  134 VAL
Chi-restraints excluded: chain B residue  193 ILE
Chi-restraints excluded: chain B residue  214 ARG
Chi-restraints excluded: chain B residue  233 TYR
Chi-restraints excluded: chain B residue  246 GLU
Chi-restraints excluded: chain B residue  310 VAL
Chi-restraints excluded: chain B residue  324 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 81 optimal weight:    4.9990
   chunk 78 optimal weight:    8.9990
   chunk 34 optimal weight:    0.8980
   chunk 61 optimal weight:    3.9990
   chunk 53 optimal weight:    8.9990
   chunk 33 optimal weight:    0.9990
   chunk 47 optimal weight:   10.0000
   chunk 66 optimal weight:    3.9990
   chunk 25 optimal weight:    1.9990
   chunk 0 optimal weight:    5.9990
   chunk 80 optimal weight:    2.9990
   overall best weight:    2.1788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A  87 ASN
A  93 GLN
A 131 ASN
A 186 GLN
A 256 GLN
A 366 GLN
** B  87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.130195 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.101638 restraints weight = 14850.523|
|-----------------------------------------------------------------------------|
r_work (start): 0.3307 rms_B_bonded: 1.92
r_work: 0.3165 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.3007 rms_B_bonded: 4.85 restraints_weight: 0.2500
r_work (final): 0.3007
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8141
moved from start:          1.3442

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   9997  Z= 0.241
  Angle     :  0.590   7.212  14143  Z= 0.318
  Chirality :  0.040   0.158   1628
  Planarity :  0.005   0.067   1293
  Dihedral  : 21.496  82.417   2931
  Min Nonbonded Distance : 2.014

Molprobity Statistics.
  All-atom Clashscore : 8.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.38 %
    Favored  : 97.62 %
  Rotamer:
    Outliers :  5.07 %
    Allowed  : 32.17 %
    Favored  : 62.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.22 (0.29), residues: 797
  helix:  2.42 (0.26), residues: 379
  sheet: -0.04 (0.40), residues: 153
  loop : -1.09 (0.35), residues: 265

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP B 201 
 HIS   0.006   0.001   HIS A 278 
 PHE   0.009   0.001   PHE A 336 
 TYR   0.015   0.001   TYR B 185 
 ARG   0.017   0.001   ARG A 111 

*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1594 Ramachandran restraints generated.
    797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1594 Ramachandran restraints generated.
    797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  243 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 208
  time to evaluate  : 0.914 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 SER cc_start: 0.8255 (OUTLIER) cc_final: 0.8031 (t)
REVERT: A  130 GLU cc_start: 0.7955 (tm-30) cc_final: 0.7700 (tm-30)
REVERT: A  137 MET cc_start: 0.8574 (mmm) cc_final: 0.8227 (mmm)
REVERT: A  155 GLN cc_start: 0.8687 (mm-40) cc_final: 0.8345 (mm-40)
REVERT: A  161 ARG cc_start: 0.8187 (mmt90) cc_final: 0.7901 (mtp85)
REVERT: A  246 GLU cc_start: 0.7962 (mp0) cc_final: 0.7749 (mp0)
REVERT: A  261 ARG cc_start: 0.8437 (OUTLIER) cc_final: 0.8118 (ttp80)
REVERT: A  270 TYR cc_start: 0.8532 (p90) cc_final: 0.8073 (p90)
REVERT: A  351 TYR cc_start: 0.7471 (OUTLIER) cc_final: 0.7192 (t80)
REVERT: A  406 ARG cc_start: 0.8025 (OUTLIER) cc_final: 0.7684 (ttp80)
REVERT: A  420 SER cc_start: 0.7928 (m) cc_final: 0.7647 (p)
REVERT: B    6 ARG cc_start: 0.8176 (mtm-85) cc_final: 0.7840 (ttp-110)
REVERT: B   44 GLU cc_start: 0.8520 (tp30) cc_final: 0.8285 (tp30)
REVERT: B   54 ASP cc_start: 0.7303 (m-30) cc_final: 0.7100 (m-30)
REVERT: B  118 SER cc_start: 0.8707 (t) cc_final: 0.8453 (p)
REVERT: B  120 LYS cc_start: 0.8996 (mmmm) cc_final: 0.8768 (tppp)
REVERT: B  157 MET cc_start: 0.8666 (mpp) cc_final: 0.8307 (mpp)
REVERT: B  177 MET cc_start: 0.8120 (mmp) cc_final: 0.7729 (tpp)
REVERT: B  178 ASP cc_start: 0.7787 (m-30) cc_final: 0.7437 (m-30)
REVERT: B  233 TYR cc_start: 0.8084 (OUTLIER) cc_final: 0.7445 (t80)
REVERT: B  249 GLU cc_start: 0.7101 (tp30) cc_final: 0.6870 (tp30)
REVERT: B  289 GLN cc_start: 0.7541 (tp40) cc_final: 0.7329 (tp40)
REVERT: B  315 LYS cc_start: 0.8486 (tttt) cc_final: 0.8068 (tttm)
  outliers start: 35
  outliers final: 18
  residues processed: 228
  average time/residue: 1.5803
  time to fit residues: 379.5929
Evaluate side-chains
  223 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 200
  time to evaluate  : 0.830 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 SER
Chi-restraints excluded: chain A residue   70 ASN
Chi-restraints excluded: chain A residue  114 MET
Chi-restraints excluded: chain A residue  126 ASP
Chi-restraints excluded: chain A residue  132 ILE
Chi-restraints excluded: chain A residue  221 ILE
Chi-restraints excluded: chain A residue  257 VAL
Chi-restraints excluded: chain A residue  261 ARG
Chi-restraints excluded: chain A residue  283 ARG
Chi-restraints excluded: chain A residue  351 TYR
Chi-restraints excluded: chain A residue  394 CYS
Chi-restraints excluded: chain A residue  406 ARG
Chi-restraints excluded: chain B residue   31 THR
Chi-restraints excluded: chain B residue   39 THR
Chi-restraints excluded: chain B residue  114 MET
Chi-restraints excluded: chain B residue  132 ILE
Chi-restraints excluded: chain B residue  180 ILE
Chi-restraints excluded: chain B residue  193 ILE
Chi-restraints excluded: chain B residue  196 ASP
Chi-restraints excluded: chain B residue  214 ARG
Chi-restraints excluded: chain B residue  233 TYR
Chi-restraints excluded: chain B residue  246 GLU
Chi-restraints excluded: chain B residue  310 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 52 optimal weight:   10.0000
   chunk 40 optimal weight:    2.9990
   chunk 71 optimal weight:    2.9990
   chunk 64 optimal weight:    6.9990
   chunk 31 optimal weight:    6.9990
   chunk 24 optimal weight:    0.8980
   chunk 51 optimal weight:   10.0000
   chunk 6 optimal weight:    0.1980
   chunk 55 optimal weight:    0.0770
   chunk 43 optimal weight:    6.9990
   chunk 41 optimal weight:    0.0040
   overall best weight:    0.8352

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A  93 GLN
A 377 ASN
B  87 ASN
** B 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.133978 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.105671 restraints weight = 14902.495|
|-----------------------------------------------------------------------------|
r_work (start): 0.3360 rms_B_bonded: 1.90
r_work: 0.3221 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.3066 rms_B_bonded: 4.86 restraints_weight: 0.2500
r_work (final): 0.3066
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8082
moved from start:          1.3568

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9997  Z= 0.158
  Angle     :  0.558   7.255  14143  Z= 0.301
  Chirality :  0.038   0.161   1628
  Planarity :  0.004   0.072   1293
  Dihedral  : 21.490  82.921   2931
  Min Nonbonded Distance : 2.051

Molprobity Statistics.
  All-atom Clashscore : 8.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.13 %
    Favored  : 97.87 %
  Rotamer:
    Outliers :  3.48 %
    Allowed  : 34.49 %
    Favored  : 62.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.54 (0.30), residues: 797
  helix:  2.79 (0.26), residues: 371
  sheet: -0.03 (0.40), residues: 155
  loop : -0.88 (0.35), residues: 271

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  45 
 HIS   0.003   0.001   HIS B 194 
 PHE   0.007   0.001   PHE A 336 
 TYR   0.011   0.001   TYR B 402 
 ARG   0.018   0.001   ARG A 111 

*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1594 Ramachandran restraints generated.
    797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1594 Ramachandran restraints generated.
    797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  232 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 208
  time to evaluate  : 0.839 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  129 LYS cc_start: 0.9321 (ttmm) cc_final: 0.9042 (ttmm)
REVERT: A  130 GLU cc_start: 0.7998 (tm-30) cc_final: 0.7770 (tm-30)
REVERT: A  137 MET cc_start: 0.8499 (mmm) cc_final: 0.8189 (mmm)
REVERT: A  155 GLN cc_start: 0.8715 (mm-40) cc_final: 0.8408 (mm-40)
REVERT: A  161 ARG cc_start: 0.8150 (mmt90) cc_final: 0.7866 (mtp85)
REVERT: A  261 ARG cc_start: 0.8381 (OUTLIER) cc_final: 0.8051 (ttp80)
REVERT: A  270 TYR cc_start: 0.8476 (p90) cc_final: 0.7681 (p90)
REVERT: A  291 ARG cc_start: 0.7945 (ttp-170) cc_final: 0.7556 (ttm170)
REVERT: A  351 TYR cc_start: 0.7354 (OUTLIER) cc_final: 0.7147 (t80)
REVERT: A  406 ARG cc_start: 0.7931 (OUTLIER) cc_final: 0.7468 (ttp80)
REVERT: A  410 ILE cc_start: 0.8099 (mm) cc_final: 0.7824 (mp)
REVERT: A  420 SER cc_start: 0.7971 (m) cc_final: 0.7681 (p)
REVERT: B    6 ARG cc_start: 0.8200 (mtm-85) cc_final: 0.7994 (ttp-110)
REVERT: B   37 LYS cc_start: 0.8586 (tptm) cc_final: 0.8363 (tptm)
REVERT: B   44 GLU cc_start: 0.8454 (tp30) cc_final: 0.8222 (tp30)
REVERT: B   69 THR cc_start: 0.9028 (OUTLIER) cc_final: 0.8804 (p)
REVERT: B  129 LYS cc_start: 0.8346 (ptmt) cc_final: 0.8023 (pttt)
REVERT: B  157 MET cc_start: 0.8619 (mpp) cc_final: 0.8237 (mpp)
REVERT: B  177 MET cc_start: 0.8284 (mmp) cc_final: 0.7914 (tpp)
REVERT: B  178 ASP cc_start: 0.7843 (m-30) cc_final: 0.7501 (m-30)
REVERT: B  190 SER cc_start: 0.8664 (OUTLIER) cc_final: 0.8447 (m)
REVERT: B  214 ARG cc_start: 0.6805 (OUTLIER) cc_final: 0.6583 (ptp-110)
REVERT: B  233 TYR cc_start: 0.7907 (OUTLIER) cc_final: 0.7367 (t80)
REVERT: B  249 GLU cc_start: 0.7016 (tp30) cc_final: 0.6713 (tp30)
REVERT: B  289 GLN cc_start: 0.7510 (tp40) cc_final: 0.7246 (tp40)
REVERT: B  315 LYS cc_start: 0.8419 (tttt) cc_final: 0.8101 (tttm)
REVERT: B  335 ARG cc_start: 0.7513 (mtt-85) cc_final: 0.7116 (mtt-85)
REVERT: B  346 GLN cc_start: 0.7928 (tt0) cc_final: 0.7679 (tp40)
REVERT: B  362 LYS cc_start: 0.8636 (mmmm) cc_final: 0.8353 (mmmm)
  outliers start: 24
  outliers final: 7
  residues processed: 221
  average time/residue: 1.6023
  time to fit residues: 373.1118
Evaluate side-chains
  221 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 207
  time to evaluate  : 0.781 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 GLN
Chi-restraints excluded: chain A residue   70 ASN
Chi-restraints excluded: chain A residue  261 ARG
Chi-restraints excluded: chain A residue  283 ARG
Chi-restraints excluded: chain A residue  351 TYR
Chi-restraints excluded: chain A residue  394 CYS
Chi-restraints excluded: chain A residue  406 ARG
Chi-restraints excluded: chain B residue   31 THR
Chi-restraints excluded: chain B residue   69 THR
Chi-restraints excluded: chain B residue  132 ILE
Chi-restraints excluded: chain B residue  190 SER
Chi-restraints excluded: chain B residue  214 ARG
Chi-restraints excluded: chain B residue  233 TYR
Chi-restraints excluded: chain B residue  246 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 8 optimal weight:    5.9990
   chunk 35 optimal weight:    3.9990
   chunk 62 optimal weight:    3.9990
   chunk 59 optimal weight:    8.9990
   chunk 34 optimal weight:    3.9990
   chunk 14 optimal weight:    4.9990
   chunk 4 optimal weight:    3.9990
   chunk 37 optimal weight:    9.9990
   chunk 81 optimal weight:    8.9990
   chunk 47 optimal weight:   10.0000
   chunk 13 optimal weight:    2.9990
   overall best weight:    3.7990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A  87 ASN
A  93 GLN
A 131 ASN
A 186 GLN
A 256 GLN
A 366 GLN
** B  87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.127579 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.099550 restraints weight = 14532.884|
|-----------------------------------------------------------------------------|
r_work (start): 0.3264 rms_B_bonded: 1.86
r_work: 0.3124 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.2966 rms_B_bonded: 4.71 restraints_weight: 0.2500
r_work (final): 0.2966
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8182
moved from start:          1.3872

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.046   9997  Z= 0.376
  Angle     :  0.666   7.331  14143  Z= 0.354
  Chirality :  0.044   0.184   1628
  Planarity :  0.005   0.080   1293
  Dihedral  : 21.568  85.318   2931
  Min Nonbonded Distance : 1.922

Molprobity Statistics.
  All-atom Clashscore : 8.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  4.20 %
    Allowed  : 35.80 %
    Favored  : 60.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.03 (0.29), residues: 797
  helix:  2.23 (0.26), residues: 379
  sheet: -0.17 (0.39), residues: 159
  loop : -1.11 (0.35), residues: 259

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B  45 
 HIS   0.006   0.001   HIS B  72 
 PHE   0.013   0.002   PHE B  48 
 TYR   0.016   0.002   TYR B 119 
 ARG   0.020   0.001   ARG A 111 

*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1594 Ramachandran restraints generated.
    797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1594 Ramachandran restraints generated.
    797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  233 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 204
  time to evaluate  : 1.017 
Fit side-chains
   revert: symmetry clash
REVERT: A  130 GLU cc_start: 0.8033 (tm-30) cc_final: 0.7773 (tm-30)
REVERT: A  137 MET cc_start: 0.8677 (mmm) cc_final: 0.8329 (mmm)
REVERT: A  155 GLN cc_start: 0.8720 (mm-40) cc_final: 0.8391 (mm-40)
REVERT: A  161 ARG cc_start: 0.8256 (mmt90) cc_final: 0.7978 (mtp85)
REVERT: A  228 VAL cc_start: 0.8688 (m) cc_final: 0.8476 (p)
REVERT: A  269 LYS cc_start: 0.8656 (pttt) cc_final: 0.8333 (pttt)
REVERT: A  355 GLU cc_start: 0.8360 (tp30) cc_final: 0.8106 (tp30)
REVERT: A  420 SER cc_start: 0.7994 (m) cc_final: 0.7701 (p)
REVERT: B    6 ARG cc_start: 0.8212 (mtm-85) cc_final: 0.7857 (ttp-110)
REVERT: B   69 THR cc_start: 0.9049 (OUTLIER) cc_final: 0.8817 (p)
REVERT: B  114 MET cc_start: 0.9105 (OUTLIER) cc_final: 0.8669 (ptp)
REVERT: B  118 SER cc_start: 0.8813 (t) cc_final: 0.8612 (p)
REVERT: B  157 MET cc_start: 0.8704 (mpp) cc_final: 0.8388 (mpp)
REVERT: B  177 MET cc_start: 0.8242 (mmp) cc_final: 0.8021 (tpp)
REVERT: B  178 ASP cc_start: 0.7955 (m-30) cc_final: 0.7590 (m-30)
REVERT: B  193 ILE cc_start: 0.8717 (pt) cc_final: 0.8475 (mt)
REVERT: B  200 LYS cc_start: 0.8242 (mmmt) cc_final: 0.7944 (mmmt)
REVERT: B  214 ARG cc_start: 0.7291 (OUTLIER) cc_final: 0.6950 (ptp-110)
REVERT: B  222 MET cc_start: 0.8349 (OUTLIER) cc_final: 0.7858 (tmm)
REVERT: B  233 TYR cc_start: 0.8161 (OUTLIER) cc_final: 0.7542 (t80)
REVERT: B  249 GLU cc_start: 0.7099 (tp30) cc_final: 0.6799 (tp30)
REVERT: B  289 GLN cc_start: 0.7651 (tp40) cc_final: 0.7328 (tp40)
REVERT: B  315 LYS cc_start: 0.8517 (tttt) cc_final: 0.8193 (tttm)
REVERT: B  335 ARG cc_start: 0.7678 (mtt-85) cc_final: 0.7237 (mtt-85)
  outliers start: 29
  outliers final: 13
  residues processed: 220
  average time/residue: 1.4596
  time to fit residues: 339.5837
Evaluate side-chains
  213 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 195
  time to evaluate  : 0.885 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 GLN
Chi-restraints excluded: chain A residue   70 ASN
Chi-restraints excluded: chain A residue   79 ILE
Chi-restraints excluded: chain A residue  126 ASP
Chi-restraints excluded: chain A residue  221 ILE
Chi-restraints excluded: chain A residue  283 ARG
Chi-restraints excluded: chain A residue  394 CYS
Chi-restraints excluded: chain B residue   31 THR
Chi-restraints excluded: chain B residue   69 THR
Chi-restraints excluded: chain B residue  114 MET
Chi-restraints excluded: chain B residue  132 ILE
Chi-restraints excluded: chain B residue  133 SER
Chi-restraints excluded: chain B residue  134 VAL
Chi-restraints excluded: chain B residue  181 LEU
Chi-restraints excluded: chain B residue  214 ARG
Chi-restraints excluded: chain B residue  222 MET
Chi-restraints excluded: chain B residue  233 TYR
Chi-restraints excluded: chain B residue  246 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 41 optimal weight:    3.9990
   chunk 2 optimal weight:    1.9990
   chunk 28 optimal weight:    1.9990
   chunk 91 optimal weight:    1.9990
   chunk 13 optimal weight:    5.9990
   chunk 10 optimal weight:    2.9990
   chunk 8 optimal weight:    4.9990
   chunk 1 optimal weight:    0.8980
   chunk 47 optimal weight:   10.0000
   chunk 35 optimal weight:    0.9980
   chunk 77 optimal weight:    2.9990
   overall best weight:    1.5786

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A  93 GLN
A 139 HIS
A 186 GLN
A 366 GLN
A 377 ASN
** B  87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 377 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.130787 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.102680 restraints weight = 14867.819|
|-----------------------------------------------------------------------------|
r_work (start): 0.3317 rms_B_bonded: 1.87
r_work: 0.3176 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work: 0.3018 rms_B_bonded: 4.78 restraints_weight: 0.2500
r_work (final): 0.3018
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8137
moved from start:          1.3981

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   9997  Z= 0.214
  Angle     :  0.608   7.613  14143  Z= 0.327
  Chirality :  0.040   0.216   1628
  Planarity :  0.005   0.078   1293
  Dihedral  : 21.524  80.994   2931
  Min Nonbonded Distance : 2.037

Molprobity Statistics.
  All-atom Clashscore : 8.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  3.62 %
    Allowed  : 37.10 %
    Favored  : 59.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.25 (0.30), residues: 797
  helix:  2.48 (0.26), residues: 371
  sheet: -0.13 (0.39), residues: 158
  loop : -0.95 (0.36), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP B  45 
 HIS   0.004   0.001   HIS A 278 
 PHE   0.007   0.001   PHE A 336 
 TYR   0.012   0.001   TYR A  59 
 ARG   0.020   0.001   ARG A 111 

********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1594 Ramachandran restraints generated.
    797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1594 Ramachandran restraints generated.
    797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  222 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 197
  time to evaluate  : 0.867 
Fit side-chains
   revert: symmetry clash
REVERT: A   30 GLU cc_start: 0.7614 (mm-30) cc_final: 0.7363 (mt-10)
REVERT: A  130 GLU cc_start: 0.7986 (tm-30) cc_final: 0.7734 (tm-30)
REVERT: A  137 MET cc_start: 0.8650 (mmm) cc_final: 0.8301 (mmm)
REVERT: A  155 GLN cc_start: 0.8731 (mm-40) cc_final: 0.8415 (mm-40)
REVERT: A  161 ARG cc_start: 0.8223 (mmt90) cc_final: 0.7931 (mtp85)
REVERT: A  210 GLU cc_start: 0.8016 (mp0) cc_final: 0.7362 (mp0)
REVERT: A  228 VAL cc_start: 0.8653 (m) cc_final: 0.8415 (p)
REVERT: A  269 LYS cc_start: 0.8645 (pttt) cc_final: 0.8366 (pttt)
REVERT: A  291 ARG cc_start: 0.8069 (ttp-170) cc_final: 0.7849 (tpp80)
REVERT: A  420 SER cc_start: 0.7864 (m) cc_final: 0.7570 (p)
REVERT: B    1 MET cc_start: 0.6687 (mtp) cc_final: 0.6262 (mmm)
REVERT: B    6 ARG cc_start: 0.8199 (mtm-85) cc_final: 0.7875 (ttp-110)
REVERT: B   31 THR cc_start: 0.8263 (OUTLIER) cc_final: 0.7982 (p)
REVERT: B  114 MET cc_start: 0.9086 (OUTLIER) cc_final: 0.8486 (ptp)
REVERT: B  118 SER cc_start: 0.8701 (t) cc_final: 0.8459 (p)
REVERT: B  122 ASP cc_start: 0.8060 (OUTLIER) cc_final: 0.7776 (t0)
REVERT: B  157 MET cc_start: 0.8634 (mpp) cc_final: 0.8338 (mpp)
REVERT: B  177 MET cc_start: 0.8249 (mmp) cc_final: 0.8014 (tpp)
REVERT: B  178 ASP cc_start: 0.7938 (m-30) cc_final: 0.7584 (m-30)
REVERT: B  193 ILE cc_start: 0.8716 (pt) cc_final: 0.8497 (mt)
REVERT: B  200 LYS cc_start: 0.8206 (mmmt) cc_final: 0.7917 (mmmt)
REVERT: B  214 ARG cc_start: 0.7170 (OUTLIER) cc_final: 0.6796 (ptp-110)
REVERT: B  233 TYR cc_start: 0.8147 (OUTLIER) cc_final: 0.7532 (t80)
REVERT: B  249 GLU cc_start: 0.7006 (tp30) cc_final: 0.6767 (tp30)
REVERT: B  289 GLN cc_start: 0.7631 (tp40) cc_final: 0.7324 (tp40)
REVERT: B  315 LYS cc_start: 0.8454 (tttt) cc_final: 0.8230 (tttm)
REVERT: B  335 ARG cc_start: 0.7671 (mtt-85) cc_final: 0.7267 (mtt-85)
REVERT: B  349 ILE cc_start: 0.7404 (mm) cc_final: 0.6975 (tt)
REVERT: B  359 LYS cc_start: 0.7560 (tptp) cc_final: 0.7219 (tptp)
REVERT: B  377 ASN cc_start: 0.7791 (OUTLIER) cc_final: 0.7567 (p0)
  outliers start: 25
  outliers final: 9
  residues processed: 208
  average time/residue: 1.5260
  time to fit residues: 335.0675
Evaluate side-chains
  210 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 195
  time to evaluate  : 0.901 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 GLN
Chi-restraints excluded: chain A residue   62 SER
Chi-restraints excluded: chain A residue   70 ASN
Chi-restraints excluded: chain A residue  114 MET
Chi-restraints excluded: chain A residue  126 ASP
Chi-restraints excluded: chain A residue  394 CYS
Chi-restraints excluded: chain B residue   31 THR
Chi-restraints excluded: chain B residue  114 MET
Chi-restraints excluded: chain B residue  122 ASP
Chi-restraints excluded: chain B residue  132 ILE
Chi-restraints excluded: chain B residue  214 ARG
Chi-restraints excluded: chain B residue  233 TYR
Chi-restraints excluded: chain B residue  246 GLU
Chi-restraints excluded: chain B residue  343 TYR
Chi-restraints excluded: chain B residue  377 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 7 optimal weight:    3.9990
   chunk 1 optimal weight:    4.9990
   chunk 58 optimal weight:    4.9990
   chunk 12 optimal weight:    2.9990
   chunk 67 optimal weight:   10.0000
   chunk 34 optimal weight:    1.9990
   chunk 69 optimal weight:    0.8980
   chunk 60 optimal weight:    6.9990
   chunk 86 optimal weight:    9.9990
   chunk 37 optimal weight:    2.9990
   chunk 72 optimal weight:    6.9990
   overall best weight:    2.5788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A  93 GLN
A 139 HIS
A 186 GLN
A 256 GLN
A 366 GLN
B  70 ASN
** B  87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.129118 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.101101 restraints weight = 14771.794|
|-----------------------------------------------------------------------------|
r_work (start): 0.3290 rms_B_bonded: 1.86
r_work: 0.3147 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.2988 rms_B_bonded: 4.78 restraints_weight: 0.2500
r_work (final): 0.2988
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8167
moved from start:          1.4077

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036   9997  Z= 0.281
  Angle     :  0.633   9.159  14143  Z= 0.337
  Chirality :  0.041   0.215   1628
  Planarity :  0.005   0.084   1293
  Dihedral  : 21.549  82.407   2931
  Min Nonbonded Distance : 1.960

Molprobity Statistics.
  All-atom Clashscore : 7.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.14 %
    Favored  : 96.86 %
  Rotamer:
    Outliers :  3.48 %
    Allowed  : 37.10 %
    Favored  : 59.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.24 (0.30), residues: 797
  helix:  2.43 (0.26), residues: 371
  sheet: -0.10 (0.40), residues: 158
  loop : -0.90 (0.36), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP B  45 
 HIS   0.005   0.001   HIS A 278 
 PHE   0.011   0.002   PHE B 236 
 TYR   0.017   0.002   TYR B 402 
 ARG   0.020   0.001   ARG A 111 

===============================================================================
Job complete
usr+sys time: 7878.43 seconds
wall clock time: 139 minutes 28.78 seconds (8368.78 seconds total)